OTR: GO:0070389_!_chaperone_cofactor-dependent_protein_refolding vs GO:0051085 ! chaperone mediated protein folding requiring cofactor

[gocentral]

Checking to see if this is what is meant: GO:0070389_!_chaperone_cofactor-dependent_protein_refolding cofactor/cochaperone stimulates refolding but is not required

GO:0051085 ! chaperone mediated protein folding requiring cofactor cofactor/cochaperone is required to observe refolding above background

In practice, I'm not sure of examples where annotation of a chaperone or cochaperone would use this distinction, as I believe the difference is seen between classes of substrates. In cases where the co-chaperone is always required, it might be viewed as a part of the chaperone, rather than as a cochaperone.

I will ask my chaperone expert to look at this.

Reported by: jimhu

Original Ticket: geneontology/ontology-requests/10536

[gocentral]

• assigned_to: David Osumi-Sutherland

Original comment by: dosumis

[gocentral]

Hi Jim, Did you get any expert feedback on this. Difficult to see what edits might be required without some more info.
Cheers, David

Original comment by: dosumis

[gocentral]

Hi David,

Sorry, I meant to send this along but got distracted.

Jim

Hi Jim:

Your assessment is right on target. A label about chaperone/co-chaperone/cofactor-dependent folding has nothing to do with a particular chaperone system and everything to do with the specific protein. If this annotation terminology is meant to apply to chaperones themselves, it makes no sense to me. If the terminology is meant to apply to different client proteins, then it would make more sense. One could, in principle, LOSELY classify every protein in an organism as highly molecular chaperone dependent, moderately chaperone dependent or independent. To be reasonably accurate, you would really require a term like this for each of the major chaperone systems, for each putative client protein. There have been enough proteomics done with the Hsp60s to make a reasonable stab at this. Not sure anyone has done a sufficiently complete and redundant analysis of the other major systems...

Hope this helps!

Best,

hays

Hays Rye Associate Professor Dept. of Biochemistry and Biophysics Texas A&M University 2128 TAMU College Station, TX 77843

On Jan 24, 2014, at 6:34 AM, David Osumi-Sutherland wrote:

Hi Jim, Did you get any expert feedback on this. Difficult to see what edits might be required without some more info. Cheers, David

[ontology-requests:#10536] OTR: GO:0070389_!_chaperone_cofactor-dependent_protein_refolding vs GO:0051085 ! chaperone mediated protein folding requiring cofactor

Status: open Created: Tue Nov 19, 2013 05:59 AM UTC by Jim Hu Last Updated: Wed Nov 20, 2013 10:43 AM UTC Owner: David Osumi-Sutherland

Checking to see if this is what is meant: GO:0070389_!_chaperone_cofactor-dependent_protein_refolding cofactor/cochaperone stimulates refolding but is not required

GO:0051085 ! chaperone mediated protein folding requiring cofactor cofactor/cochaperone is required to observe refolding above background

In practice, I'm not sure of examples where annotation of a chaperone or cochaperone would use this distinction, as I believe the difference is seen between classes of substrates. In cases where the co-chaperone is always required, it might be viewed as a part of the chaperone, rather than as a cochaperone.

I will ask my chaperone expert to look at this.

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Jim Hu Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054

Original comment by: jimhu

[ValWood]

Hi Jim, Is this still on your radar?

Best Val

[pgaudet]

There are EXP annotations by EcoCyc @keseler MGI @hdrabkin UniProt @ggeorghiou RDG @slaulederkind

Can you please check if based on your annotations these two terms are different? There are many protein families annotated to both, sounds like a merge is appropriate.

Thanks, Pascale

[amandamackie]

EcoCyc@keseler passed this query on to me. The terms appear to have been used interchangeably in EcoCyc and so a merge would be OK for us.

Amanda

[slaulederkind]

RGD ended up with an annotation to only the refolding term. There is probably no practical difference between the two terms.

[ggeorghiou]

I've reviewed the annotations for CAFA and UniProt and both terms are used interchangeably. A merge is ok by me.

[pgaudet]

Looks like the distinction was between protein folding and protein refolding; is this important ?

Thanks, Pascale

[pgaudet]

Hi @jimhu-tamu (1) I merged GO:0070389_!_chaperone_cofactor-dependent_protein_refolding with GO:0051085 ! chaperone mediated protein folding requiring cofactor but I am not sure this is what was being discussed. The two terms above concern protein folding and refolding. I don't know whether there should be a distinction - is folding and refolding done by separate pathways ?

(2) What I am reading above is that there is no such thing as a co-chaperone 'pathway', so there is no way to classify chaperone versus co-chaperones.

If this is right, then we should rather merge GO:0051085 chaperone cofactor-dependent protein refolding and sibling GO:0051086 chaperone mediated protein folding independent of cofactor with their parent GO:0061077 chaperone-mediated protein folding

What do you think ?

Thanks, Pascale

[RLovering]

Hi

it is not clear to me what changes you are making, however I hope this will mean that de-novo folding and refolding terms remain distinct.

Thanks

Ruth